PCORnet CDM

Category: Distributed clinical research network CDM

The PCORnet Common Data Model organizes patient, encounter, diagnosis, procedure, laboratory, medication, and related data into a shared table structure. Convert-Pheno reads exported PCORnet CDM tables; it does not connect to a live database. The route is tested with synthetic fixtures. Exports from additional PCORnet networks may expose source conventions not represented by those fixtures.

RoleInput

Accepted inputCSV/TSV tables, directory, or ZIP package

Main outputBFF, PXF, OMOP-CDM

ProcessingGrouped by PATID in memory

Clinical-domain tables are joined to DEMOGRAPHIC by PATID before target conversion

What You Need

Provide UTF-8 CSV or TSV table exports, either individually, in a directory, or inside one ZIP package. Gzip-compressed table files are also accepted. DEMOGRAPHIC is required.

Table group	Supported tables
person	DEMOGRAPHIC, DEATH
encounters and conditions	ENCOUNTER, DIAGNOSIS, CONDITION
procedures and immunization	PROCEDURES, IMMUNIZATION
observations	LAB_RESULT_CM, VITAL, OBS_CLIN, OBS_GEN
medications	PRESCRIBING, DISPENSING, MED_ADMIN, EXTERNAL_MEDS

convert-pheno \
  -ipcornet pcornet-tables.zip \
  -obff individuals.json

Use -opxf phenopackets.json for PXF, or -oomop --out-dir omop_out/ --ohdsi-db for OMOP-CDM tables. The clinical mapping is built in. For entity-aware BFF output, an optional compact Mapping V2 file can name the synthesized dataset and cohort.

What Is Converted

PCORnet content	Main BFF target
DEMOGRAPHIC, DEATH	individual identity, demographics, and vital status
DIAGNOSIS, CONDITION	diseases
PROCEDURES, IMMUNIZATION	interventionsOrProcedures
LAB_RESULT_CM, VITAL, OBS_CLIN	measures
medication tables	treatments
OBS_GEN	phenotypicFeatures
encounter links	private _visit context on mapped events

HISPANIC or another explicit ethnicity field can populate BFF ethnicity. RACE remains in source provenance because race and ethnicity are not treated as interchangeable concepts.

Terminology And Source Data

Recognized ICD-10-CM, SNOMED CT, LOINC, RxNorm, NDC, CVX, CPT, and HCPCS codes are retained as CURIEs. Ambiguous source categories remain PCORnet: terms rather than receiving an unverified crosswalk. For OMOP output, use --term-audit terminology.xlsx to review OHDSI vocabulary resolution.

Raw rows are retained under info.pcornet by default. Use --no-source-info to omit them while retaining the converted fields.

Current Boundaries

Input is non-streaming and must fit in memory. Support follows the listed PCORnet tables and their standard columns; network-specific extensions require independent review.

For the field-level contract, see PCORnet CDM to BFF.